Hello,
Naively, Perhaps the issue is that the molecule used to generate the .cif
restraints does not have the hydrogens in the right place/ right
hybridization?
My suggestion would be to check it i.e. with Avogadro or any other chemical
structure editor.
Cheers
Maxime
Le jeu. 7 janv. 2021 à 14:04, Pavel Afonine
Hi Sharan,
I'm guessing your are over-relying on graphic representations of your molecules which is discussed here to some extent:
http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10
What really matters is that the ligand fits the map and its geometry matches what's expected.
Pavel
On 1/7/21 10:20, Sharan Karade wrote:
Hello all,
I hope everybody is doing well. Happy New Year 2021!!!
I am stuck with some unusual behavior of restrain files generated by Phenix.ReadySet. I crystallized the protein with ligands which have double bonds between the atoms. As I see clear electron density for the ligand, I drew a ligand molecule in Coot (Ligand builder) and fitted in electron density very nicely. Until here, I can see the double bonds in the modelled ligand. I generated the restrain files using Phenix.ReadySet to further proceed for refinement. Unfortunately, after refinement the double bonds were converted to single bonds. I tried to generate new restrain files and refined the model, resulting in similar output. But, fortunately in one case, the double bonds were retained after refinement also. I tried to repeat with other ligands, where I was unsuccessful to retain the double bonds.
please help me. Thank you so much.
Regards Sharan
-- Sharan Karade Postdoc-fellow IBBR-UMD, 9600 Gudelsky Dr, Rockville Maryland 20850
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